Internal solitary waves (ISWs) play a crucial role in regulating marine primary productivity, particularly in oligotrophic regions. However, although previous studies have documented ISW-induced chlorophyll (Chl) enhancement and spatial asymmetry around Dongsha Atoll (DA), their role in sustaining persistent biogeochemical asymmetry and regulating its temporal variability across multiple timescales remains poorly understood. Here, a long-term merged MODIS–SeaWiFS dataset and satellite sun-glint imagery were used to investigate the influence of ISWs on the distributions of Chl and particulate organic carbon (POC) around DA. Sun-glint imagery revealed pronounced north–south asymmetry in ISW activity, with wave occurrence in the northern region approximately four times higher than that in the southern region. Comparisons of in situ observations at Stations C1_02 and S502 with satellite-derived Chl and CMEMS-derived Chl profiles showed good agreement in both surface Chl concentrations and vertical Chl structure, confirming the reliability of the satellite-derived product. Consistent with the spatial distribution of ISWs, climatological Chl and POC concentrations remained persistently higher in the northern region. The annual cycle further exhibited a pronounced north–south contrast, with consistently elevated concentrations in the northern region, whereas the southern region varied in phase with the background field. This contrast was further amplified during summer, when the north–south differences reached 51.59% for Chl and 24.06% for POC. Moreover, both Chl and POC in the northern region exhibited a distinct semi-monthly (~14-day) bimodal pattern, corresponding to alternating intensification and weakening of ISW activity, with peak north–south differences of 44.69% and 23.63%, respectively. These results suggest that ISW-induced vertical mixing enhances the asymmetric nutrient supply to the euphotic zone and shoals the deep chlorophyll maximum (DCM), thereby promoting phytoplankton growth and organic carbon accumulation in the northern region. This study highlights the critical role of ISWs in maintaining spatial biogeochemical heterogeneity and regulating temporal variability, providing new insights into the coupling between physical processes and biogeochemical structures in oligotrophic marginal seas.